Multiple sequence alignment - TraesCS2A01G098200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G098200 chr2A 100.000 3662 0 0 1 3662 51583532 51587193 0.000000e+00 6763
1 TraesCS2A01G098200 chr2B 91.949 3304 167 45 11 3264 77170292 77173546 0.000000e+00 4536
2 TraesCS2A01G098200 chr2B 94.062 320 14 1 3343 3662 77173542 77173856 7.110000e-132 481
3 TraesCS2A01G098200 chr2B 84.579 214 26 2 2496 2703 1678618 1678830 4.790000e-49 206
4 TraesCS2A01G098200 chr2D 93.019 1676 84 13 1597 3264 49878992 49880642 0.000000e+00 2416
5 TraesCS2A01G098200 chr2D 95.903 1318 41 7 6 1318 49877334 49878643 0.000000e+00 2122
6 TraesCS2A01G098200 chr2D 92.988 328 14 3 3343 3662 49880638 49880964 1.540000e-128 470
7 TraesCS2A01G098200 chr2D 90.722 194 14 3 1315 1508 49878723 49878912 4.690000e-64 255
8 TraesCS2A01G098200 chr2D 92.784 97 6 1 3254 3349 307490079 307490175 4.930000e-29 139
9 TraesCS2A01G098200 chr4D 92.063 378 30 0 12 389 312800701 312800324 1.940000e-147 532
10 TraesCS2A01G098200 chr4D 97.674 86 1 1 3261 3345 28237894 28237809 2.950000e-31 147
11 TraesCS2A01G098200 chr4D 93.137 102 3 4 3260 3358 481110279 481110379 2.950000e-31 147
12 TraesCS2A01G098200 chr3D 87.302 378 48 0 13 390 441147394 441147771 2.020000e-117 433
13 TraesCS2A01G098200 chr3D 93.204 103 4 3 3248 3348 203684643 203684542 8.190000e-32 148
14 TraesCS2A01G098200 chr3B 86.772 378 47 1 13 390 578401424 578401798 5.660000e-113 418
15 TraesCS2A01G098200 chr3A 86.243 378 52 0 13 390 581274016 581274393 9.460000e-111 411
16 TraesCS2A01G098200 chr4B 86.512 215 20 5 2496 2703 391595363 391595575 1.020000e-55 228
17 TraesCS2A01G098200 chr7A 85.915 213 21 5 2496 2701 605163720 605163510 6.160000e-53 219
18 TraesCS2A01G098200 chr7A 84.507 213 26 3 2497 2703 694564538 694564749 1.720000e-48 204
19 TraesCS2A01G098200 chr7A 96.667 90 2 1 3260 3348 83936192 83936103 8.190000e-32 148
20 TraesCS2A01G098200 chr7B 85.047 214 25 2 2496 2703 654701732 654701520 1.030000e-50 211
21 TraesCS2A01G098200 chr5B 83.251 203 34 0 178 380 66053295 66053093 1.740000e-43 187
22 TraesCS2A01G098200 chr5A 83.251 203 34 0 178 380 54464334 54464536 1.740000e-43 187
23 TraesCS2A01G098200 chr5A 98.837 86 1 0 3261 3346 355734140 355734055 1.760000e-33 154
24 TraesCS2A01G098200 chr5D 82.266 203 36 0 178 380 64134550 64134752 3.760000e-40 176
25 TraesCS2A01G098200 chr7D 98.824 85 1 0 3261 3345 414277599 414277683 6.330000e-33 152
26 TraesCS2A01G098200 chr6D 94.737 95 2 3 3261 3352 6968019 6967925 1.060000e-30 145
27 TraesCS2A01G098200 chr6B 95.604 91 2 2 3260 3348 617177291 617177201 1.060000e-30 145


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G098200 chr2A 51583532 51587193 3661 False 6763.00 6763 100.0000 1 3662 1 chr2A.!!$F1 3661
1 TraesCS2A01G098200 chr2B 77170292 77173856 3564 False 2508.50 4536 93.0055 11 3662 2 chr2B.!!$F2 3651
2 TraesCS2A01G098200 chr2D 49877334 49880964 3630 False 1315.75 2416 93.1580 6 3662 4 chr2D.!!$F2 3656

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
121 122 0.391661 AAGTCGACGCTGATGGCAAT 60.392 50.000 10.46 0.0 41.91 3.56 F
396 397 0.544833 ATGGCCAAATGAGCACCCAA 60.545 50.000 10.96 0.0 0.00 4.12 F
734 738 1.202348 GTTATCCTGTGCTTTGGTGCC 59.798 52.381 0.00 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1053 1086 0.112412 GCTTCTTCAGGAAACCCCCA 59.888 55.0 0.0 0.0 33.07 4.96 R
1635 1775 0.385390 AAAGGGCTGAAAGTGTTGCG 59.615 50.0 0.0 0.0 35.30 4.85 R
2673 2820 0.235926 GCAACTCAACCAGCGAAGTC 59.764 55.0 0.0 0.0 0.00 3.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 0.391661 AAGTCGACGCTGATGGCAAT 60.392 50.000 10.46 0.00 41.91 3.56
178 179 1.026718 CCCGCAAGATGAAGGACACC 61.027 60.000 0.00 0.00 43.02 4.16
355 356 2.224378 CGGTGATGGCCAGATCAACTAT 60.224 50.000 19.67 0.00 37.83 2.12
364 365 4.384647 GGCCAGATCAACTATGAGGAGTTT 60.385 45.833 0.00 0.00 37.57 2.66
394 395 0.971959 TGATGGCCAAATGAGCACCC 60.972 55.000 10.96 0.00 0.00 4.61
396 397 0.544833 ATGGCCAAATGAGCACCCAA 60.545 50.000 10.96 0.00 0.00 4.12
609 612 2.098117 GGTGTATCCTGATTGCTGTTGC 59.902 50.000 0.00 0.00 40.20 4.17
672 676 7.124901 TGACTCTTCTAGTATCAATGGAAAGCT 59.875 37.037 0.00 0.00 39.07 3.74
691 695 4.385825 AGCTGGTGTTTCGTAATTCTTCA 58.614 39.130 0.00 0.00 0.00 3.02
734 738 1.202348 GTTATCCTGTGCTTTGGTGCC 59.798 52.381 0.00 0.00 0.00 5.01
737 741 1.829533 CCTGTGCTTTGGTGCCTGT 60.830 57.895 0.00 0.00 0.00 4.00
802 812 6.592220 TGTGATGCTGGATGAAATTTGAAATG 59.408 34.615 0.00 0.00 0.00 2.32
962 979 3.201045 GTCCTCTTAAGGCCTGGAATTCT 59.799 47.826 5.69 0.00 43.02 2.40
974 991 1.881973 TGGAATTCTCTGTGCTTGTGC 59.118 47.619 5.23 0.00 40.20 4.57
1050 1083 2.342279 CTCCACGGCTTTCGGACA 59.658 61.111 0.00 0.00 44.45 4.02
1053 1086 1.597027 CCACGGCTTTCGGACAAGT 60.597 57.895 0.00 0.00 44.45 3.16
1161 1194 6.374333 TGATAGATCCTGTTTAAGCGCTTTTT 59.626 34.615 30.13 6.65 0.00 1.94
1179 1214 4.744795 TTTTGCCTTTTGCTCTGGTTTA 57.255 36.364 0.00 0.00 42.00 2.01
1350 1467 3.415212 TGAAATCAGCACTTCTTCCAGG 58.585 45.455 0.00 0.00 0.00 4.45
1364 1481 2.452600 TCCAGGCTTCAGTTTGGTTT 57.547 45.000 0.00 0.00 32.51 3.27
1367 1484 2.031120 CAGGCTTCAGTTTGGTTTCCA 58.969 47.619 0.00 0.00 0.00 3.53
1378 1495 3.370840 TTGGTTTCCAGCTAGCATCAT 57.629 42.857 18.83 0.00 33.81 2.45
1392 1509 5.049818 GCTAGCATCATTCATGTGTTCCTAC 60.050 44.000 10.63 0.00 34.56 3.18
1419 1536 6.620678 CAGGATTTCACCGAATACACAAATT 58.379 36.000 0.00 0.00 34.73 1.82
1424 1541 9.274065 GATTTCACCGAATACACAAATTTAGAC 57.726 33.333 0.00 0.00 0.00 2.59
1445 1562 2.636830 GAGTGCATTGCCTATCTGTGT 58.363 47.619 6.12 0.00 0.00 3.72
1478 1595 2.946172 AAAACGGGCCTTTCGACGGT 62.946 55.000 0.84 0.00 0.00 4.83
1510 1627 3.332968 TCTCCCAGGTAAAGGAAACCTT 58.667 45.455 0.00 0.00 45.26 3.50
1512 1643 3.057586 TCCCAGGTAAAGGAAACCTTCA 58.942 45.455 3.45 0.00 45.26 3.02
1514 1645 4.079096 TCCCAGGTAAAGGAAACCTTCAAA 60.079 41.667 3.45 0.00 45.26 2.69
1517 1648 6.495526 CCCAGGTAAAGGAAACCTTCAAAATA 59.504 38.462 3.45 0.00 45.26 1.40
1518 1649 7.015779 CCCAGGTAAAGGAAACCTTCAAAATAA 59.984 37.037 3.45 0.00 45.26 1.40
1520 1651 8.638873 CAGGTAAAGGAAACCTTCAAAATAACT 58.361 33.333 3.45 0.00 45.26 2.24
1529 1660 9.244799 GAAACCTTCAAAATAACTACTGTTTGG 57.755 33.333 0.00 0.00 37.59 3.28
1532 1663 6.295067 CCTTCAAAATAACTACTGTTTGGGGG 60.295 42.308 0.00 0.00 37.59 5.40
1552 1683 6.775594 GGGGGTGCTTATGATATTAATTCC 57.224 41.667 0.00 0.00 0.00 3.01
1553 1684 6.494059 GGGGGTGCTTATGATATTAATTCCT 58.506 40.000 0.00 0.00 0.00 3.36
1554 1685 6.378280 GGGGGTGCTTATGATATTAATTCCTG 59.622 42.308 0.00 0.00 0.00 3.86
1555 1686 7.175104 GGGGTGCTTATGATATTAATTCCTGA 58.825 38.462 0.00 0.00 0.00 3.86
1584 1717 5.660460 ACAGGATTTTCTGTGTTGAAAACC 58.340 37.500 4.82 8.20 45.08 3.27
1587 1720 7.416326 ACAGGATTTTCTGTGTTGAAAACCTAC 60.416 37.037 15.89 2.55 45.08 3.18
1635 1775 1.352687 ACTTCTCTTTCCTTCCAGGGC 59.647 52.381 0.00 0.00 35.59 5.19
1683 1823 1.435256 ACCAAGCACAGGTACTCCTT 58.565 50.000 0.00 0.00 43.07 3.36
1748 1889 5.071115 AGTTCCAGAGATATACAAAGGAGCC 59.929 44.000 0.00 0.00 0.00 4.70
1757 1898 7.349598 AGATATACAAAGGAGCCAGAAACAAT 58.650 34.615 0.00 0.00 0.00 2.71
1758 1899 5.649782 ATACAAAGGAGCCAGAAACAATG 57.350 39.130 0.00 0.00 0.00 2.82
1762 1903 3.463048 AGGAGCCAGAAACAATGGATT 57.537 42.857 0.00 0.00 40.51 3.01
1772 1913 4.773674 AGAAACAATGGATTGGATCTGCAA 59.226 37.500 4.45 0.00 41.96 4.08
1773 1914 4.730949 AACAATGGATTGGATCTGCAAG 57.269 40.909 4.45 0.00 41.96 4.01
1774 1915 3.705051 ACAATGGATTGGATCTGCAAGT 58.295 40.909 4.45 0.00 41.96 3.16
1775 1916 4.858850 ACAATGGATTGGATCTGCAAGTA 58.141 39.130 4.45 0.00 41.96 2.24
1782 1923 7.944061 TGGATTGGATCTGCAAGTAAATATTG 58.056 34.615 0.00 0.00 33.76 1.90
1810 1951 6.620877 ATTAACTGTGAGATCCAACTACCA 57.379 37.500 0.00 0.00 0.00 3.25
1989 2136 6.359804 AGTTATTCTTCAAGAGCATATGCCA 58.640 36.000 23.96 0.52 43.38 4.92
2031 2178 4.635765 GCAGAACATGTTGATACAGGCTTA 59.364 41.667 17.58 0.00 39.60 3.09
2032 2179 5.220739 GCAGAACATGTTGATACAGGCTTAG 60.221 44.000 17.58 0.00 39.60 2.18
2045 2192 7.780271 TGATACAGGCTTAGATCTGTCTCTAAA 59.220 37.037 5.18 0.00 42.51 1.85
2091 2238 5.440610 ACTAGGACATGGAAATTTAGGCAG 58.559 41.667 0.00 0.00 0.00 4.85
2094 2241 4.023291 GGACATGGAAATTTAGGCAGGAA 58.977 43.478 0.00 0.00 0.00 3.36
2132 2279 3.077484 AGATGTCCTCCAAACCATGTG 57.923 47.619 0.00 0.00 0.00 3.21
2175 2322 6.259608 GTGGATTCTGACTAGGTTGAATGATG 59.740 42.308 9.88 0.00 30.41 3.07
2422 2569 1.035139 CAGGCTTGGTTTGCACTCTT 58.965 50.000 0.00 0.00 0.00 2.85
2434 2581 2.050144 TGCACTCTTCCCTGTCTTTCT 58.950 47.619 0.00 0.00 0.00 2.52
2435 2582 2.439507 TGCACTCTTCCCTGTCTTTCTT 59.560 45.455 0.00 0.00 0.00 2.52
2436 2583 3.070748 GCACTCTTCCCTGTCTTTCTTC 58.929 50.000 0.00 0.00 0.00 2.87
2437 2584 3.244387 GCACTCTTCCCTGTCTTTCTTCT 60.244 47.826 0.00 0.00 0.00 2.85
2441 2588 5.782845 ACTCTTCCCTGTCTTTCTTCTATGT 59.217 40.000 0.00 0.00 0.00 2.29
2600 2747 4.322567 GCCTCAAATTCAGAGAGTTCAGT 58.677 43.478 8.91 0.00 35.09 3.41
2623 2770 1.017177 TAAGGACAATGTCGGCGTGC 61.017 55.000 6.85 1.63 32.65 5.34
2642 2789 1.534595 GCAGTCAGCAGAAAACCTGAG 59.465 52.381 0.00 0.00 45.78 3.35
2673 2820 1.601171 AGCTTGAGGCAGTAGCTGG 59.399 57.895 0.00 0.00 43.25 4.85
2711 2858 1.948104 CGTTGGTGTCTGAAACCTGA 58.052 50.000 17.64 4.29 38.60 3.86
2736 2887 2.026641 TGCTTGCTTTATCCAGATGGC 58.973 47.619 0.00 0.00 34.44 4.40
2738 2889 2.626743 GCTTGCTTTATCCAGATGGCAT 59.373 45.455 0.00 0.00 34.44 4.40
2803 2955 0.804989 GTCCCGATTGCCTGTTCTTG 59.195 55.000 0.00 0.00 0.00 3.02
2819 2971 4.082125 GTTCTTGTCCTCCCATGTTCATT 58.918 43.478 0.00 0.00 0.00 2.57
2859 3011 3.854240 CAGTACACTTCGATGCTACACAG 59.146 47.826 0.00 0.00 0.00 3.66
2864 3016 3.366121 CACTTCGATGCTACACAGACAAG 59.634 47.826 0.00 0.00 0.00 3.16
3072 3224 1.302351 GACACTCTGCAGCTGCCTT 60.302 57.895 34.64 14.06 41.18 4.35
3093 3245 3.795688 ATGTGGAGCCTCTTTCTTCAA 57.204 42.857 0.00 0.00 0.00 2.69
3178 3330 5.460646 CAAACAATTAATGCCGAGTCAGTT 58.539 37.500 0.00 0.00 0.00 3.16
3211 3363 7.201938 ACCCATTGGATATAAACTGATTTGCAG 60.202 37.037 3.62 0.00 42.13 4.41
3263 3415 5.941788 AGACATTCTTCTTTGTTGGGTACT 58.058 37.500 0.00 0.00 0.00 2.73
3264 3416 5.998363 AGACATTCTTCTTTGTTGGGTACTC 59.002 40.000 0.00 0.00 0.00 2.59
3265 3417 5.070685 ACATTCTTCTTTGTTGGGTACTCC 58.929 41.667 0.00 0.00 0.00 3.85
3275 3427 2.361771 GGTACTCCCTCCGTCCCA 59.638 66.667 0.00 0.00 0.00 4.37
3276 3428 1.305549 GGTACTCCCTCCGTCCCAA 60.306 63.158 0.00 0.00 0.00 4.12
3277 3429 0.906282 GGTACTCCCTCCGTCCCAAA 60.906 60.000 0.00 0.00 0.00 3.28
3278 3430 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
3279 3431 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
3280 3432 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3281 3433 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3282 3434 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3283 3435 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3284 3436 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3285 3437 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
3286 3438 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
3287 3439 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
3288 3440 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
3289 3441 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
3290 3442 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
3291 3443 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
3292 3444 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
3293 3445 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
3294 3446 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
3295 3447 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
3296 3448 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
3297 3449 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
3298 3450 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
3299 3451 8.402472 CCAAAATAAGTGACTCAACTTTGTACA 58.598 33.333 0.00 0.00 40.77 2.90
3300 3452 9.781834 CAAAATAAGTGACTCAACTTTGTACAA 57.218 29.630 3.59 3.59 40.77 2.41
3318 3470 7.709269 TGTACAAAGCTAGTACAAAGTTGAG 57.291 36.000 22.60 0.00 46.22 3.02
3319 3471 7.270047 TGTACAAAGCTAGTACAAAGTTGAGT 58.730 34.615 22.60 0.00 46.22 3.41
3320 3472 6.846325 ACAAAGCTAGTACAAAGTTGAGTC 57.154 37.500 0.00 0.00 0.00 3.36
3321 3473 6.346096 ACAAAGCTAGTACAAAGTTGAGTCA 58.654 36.000 0.00 0.00 0.00 3.41
3322 3474 6.258068 ACAAAGCTAGTACAAAGTTGAGTCAC 59.742 38.462 0.00 0.00 0.00 3.67
3323 3475 5.793030 AGCTAGTACAAAGTTGAGTCACT 57.207 39.130 0.00 0.00 0.00 3.41
3324 3476 6.163135 AGCTAGTACAAAGTTGAGTCACTT 57.837 37.500 0.00 0.00 38.74 3.16
3325 3477 7.286215 AGCTAGTACAAAGTTGAGTCACTTA 57.714 36.000 0.00 0.00 35.87 2.24
3326 3478 7.897864 AGCTAGTACAAAGTTGAGTCACTTAT 58.102 34.615 0.00 0.00 35.87 1.73
3327 3479 8.368668 AGCTAGTACAAAGTTGAGTCACTTATT 58.631 33.333 0.00 0.00 35.87 1.40
3328 3480 8.989980 GCTAGTACAAAGTTGAGTCACTTATTT 58.010 33.333 0.00 0.00 35.87 1.40
3333 3485 8.974060 ACAAAGTTGAGTCACTTATTTTAGGA 57.026 30.769 0.00 0.00 35.87 2.94
3334 3486 8.837389 ACAAAGTTGAGTCACTTATTTTAGGAC 58.163 33.333 0.00 0.00 35.87 3.85
3335 3487 7.653767 AAGTTGAGTCACTTATTTTAGGACG 57.346 36.000 0.00 0.00 35.10 4.79
3336 3488 6.164176 AGTTGAGTCACTTATTTTAGGACGG 58.836 40.000 0.00 0.00 33.84 4.79
3337 3489 5.988310 TGAGTCACTTATTTTAGGACGGA 57.012 39.130 0.00 0.00 33.84 4.69
3338 3490 5.962433 TGAGTCACTTATTTTAGGACGGAG 58.038 41.667 0.00 0.00 33.84 4.63
3339 3491 5.105473 TGAGTCACTTATTTTAGGACGGAGG 60.105 44.000 0.00 0.00 33.84 4.30
3340 3492 4.161754 AGTCACTTATTTTAGGACGGAGGG 59.838 45.833 0.00 0.00 33.84 4.30
3341 3493 4.161001 GTCACTTATTTTAGGACGGAGGGA 59.839 45.833 0.00 0.00 0.00 4.20
3342 3494 4.404715 TCACTTATTTTAGGACGGAGGGAG 59.595 45.833 0.00 0.00 0.00 4.30
3343 3495 4.161754 CACTTATTTTAGGACGGAGGGAGT 59.838 45.833 0.00 0.00 0.00 3.85
3344 3496 5.361857 CACTTATTTTAGGACGGAGGGAGTA 59.638 44.000 0.00 0.00 0.00 2.59
3345 3497 5.362143 ACTTATTTTAGGACGGAGGGAGTAC 59.638 44.000 0.00 0.00 0.00 2.73
3346 3498 3.463048 TTTTAGGACGGAGGGAGTACT 57.537 47.619 0.00 0.00 36.60 2.73
3378 3531 8.175716 GTGTTCTAAGTCGCTTGCTTAAATTAT 58.824 33.333 2.86 0.00 0.00 1.28
3415 3576 4.820897 TCATGGGCGCTTGTATAGAATAG 58.179 43.478 7.64 0.00 0.00 1.73
3454 3615 8.421673 AAGAAGCTACCGTACATCTTAATTTC 57.578 34.615 0.00 0.00 0.00 2.17
3619 3780 7.860373 GCCTTGATCAATAATTGCATTACGTTA 59.140 33.333 8.96 0.00 0.00 3.18
3650 3811 6.862209 ACATTTCTCAAACTGCTGTGTTTTA 58.138 32.000 0.00 0.00 37.98 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.463614 GGTGATGCAACCTGTAAGAGATAGAT 60.464 42.308 0.00 0.00 37.24 1.98
1 2 5.163405 GGTGATGCAACCTGTAAGAGATAGA 60.163 44.000 0.00 0.00 37.24 1.98
2 3 5.053145 GGTGATGCAACCTGTAAGAGATAG 58.947 45.833 0.00 0.00 37.24 2.08
3 4 4.469586 TGGTGATGCAACCTGTAAGAGATA 59.530 41.667 8.97 0.00 41.16 1.98
4 5 3.264193 TGGTGATGCAACCTGTAAGAGAT 59.736 43.478 8.97 0.00 41.16 2.75
121 122 0.251297 CTGGGAAGTCAATGGTGCCA 60.251 55.000 0.00 0.00 0.00 4.92
178 179 0.393673 TGAGCTCCTCCTCTGAGTCG 60.394 60.000 12.15 0.00 36.86 4.18
355 356 3.390967 TCATGACCTTGACAAACTCCTCA 59.609 43.478 0.00 0.00 0.00 3.86
364 365 0.697658 TGGCCATCATGACCTTGACA 59.302 50.000 0.00 0.00 0.00 3.58
394 395 1.227823 TGTCTTGGGAGCACGGTTG 60.228 57.895 0.00 0.00 0.00 3.77
396 397 2.743718 CTGTCTTGGGAGCACGGT 59.256 61.111 0.00 0.00 0.00 4.83
672 676 6.053005 AGAGTTGAAGAATTACGAAACACCA 58.947 36.000 0.00 0.00 0.00 4.17
712 716 2.351738 GCACCAAAGCACAGGATAACAC 60.352 50.000 0.00 0.00 0.00 3.32
734 738 2.053627 GCCATTCACAAGCGAAAACAG 58.946 47.619 0.00 0.00 0.00 3.16
737 741 1.952990 TCTGCCATTCACAAGCGAAAA 59.047 42.857 0.00 0.00 0.00 2.29
869 880 1.004610 CAACGTTGCTATCATCCAGCG 60.005 52.381 16.51 0.00 42.13 5.18
974 991 0.304705 GTGCGTGTGTTCCACTCTTG 59.695 55.000 0.00 0.00 42.20 3.02
1044 1077 1.452801 GAAACCCCCACTTGTCCGA 59.547 57.895 0.00 0.00 0.00 4.55
1050 1083 1.529744 TCTTCAGGAAACCCCCACTT 58.470 50.000 0.00 0.00 34.66 3.16
1053 1086 0.112412 GCTTCTTCAGGAAACCCCCA 59.888 55.000 0.00 0.00 33.07 4.96
1179 1214 3.512724 CCAGCAGAATTGAACTTGGGATT 59.487 43.478 0.00 0.00 0.00 3.01
1246 1281 0.603569 ATATGCCCTCGATGTCGGAC 59.396 55.000 0.00 0.00 40.29 4.79
1249 1284 1.673033 GGGAATATGCCCTCGATGTCG 60.673 57.143 12.21 0.00 45.12 4.35
1350 1467 1.683385 AGCTGGAAACCAAACTGAAGC 59.317 47.619 0.00 0.00 30.80 3.86
1364 1481 3.118149 ACACATGAATGATGCTAGCTGGA 60.118 43.478 17.23 0.00 35.15 3.86
1367 1484 3.881688 GGAACACATGAATGATGCTAGCT 59.118 43.478 17.23 0.83 35.15 3.32
1392 1509 3.063997 GTGTATTCGGTGAAATCCTGCAG 59.936 47.826 6.78 6.78 0.00 4.41
1419 1536 3.384789 AGATAGGCAATGCACTCGTCTAA 59.615 43.478 7.79 0.00 0.00 2.10
1424 1541 1.596260 CACAGATAGGCAATGCACTCG 59.404 52.381 7.79 0.40 0.00 4.18
1445 1562 3.057174 GCCCGTTTTTCACCATGTAATCA 60.057 43.478 0.00 0.00 0.00 2.57
1529 1660 6.378280 CAGGAATTAATATCATAAGCACCCCC 59.622 42.308 0.00 0.00 0.00 5.40
1532 1663 7.391554 TGCTCAGGAATTAATATCATAAGCACC 59.608 37.037 6.22 0.00 30.58 5.01
1534 1665 8.786898 GTTGCTCAGGAATTAATATCATAAGCA 58.213 33.333 6.22 6.22 33.45 3.91
1535 1666 8.786898 TGTTGCTCAGGAATTAATATCATAAGC 58.213 33.333 0.00 0.00 0.00 3.09
1537 1668 9.625747 TGTGTTGCTCAGGAATTAATATCATAA 57.374 29.630 0.00 0.00 0.00 1.90
1539 1670 8.162878 CTGTGTTGCTCAGGAATTAATATCAT 57.837 34.615 0.00 0.00 0.00 2.45
1540 1671 7.558161 CTGTGTTGCTCAGGAATTAATATCA 57.442 36.000 0.00 0.00 0.00 2.15
1552 1683 3.567164 ACAGAAAATCCTGTGTTGCTCAG 59.433 43.478 0.00 0.00 44.93 3.35
1553 1684 3.554934 ACAGAAAATCCTGTGTTGCTCA 58.445 40.909 0.00 0.00 44.93 4.26
1568 1699 6.827586 ACAAGTAGGTTTTCAACACAGAAA 57.172 33.333 0.00 0.00 35.82 2.52
1570 1701 6.646267 ACTACAAGTAGGTTTTCAACACAGA 58.354 36.000 11.57 0.00 37.49 3.41
1584 1717 9.155975 AGATGAAGCAAAACATACTACAAGTAG 57.844 33.333 5.72 5.72 33.66 2.57
1602 1741 8.956533 AGGAAAGAGAAGTTAATAGATGAAGC 57.043 34.615 0.00 0.00 0.00 3.86
1635 1775 0.385390 AAAGGGCTGAAAGTGTTGCG 59.615 50.000 0.00 0.00 35.30 4.85
1683 1823 5.824624 AGTTTGCAGAATCTGAGAGTTCAAA 59.175 36.000 15.38 10.41 32.44 2.69
1748 1889 4.158949 TGCAGATCCAATCCATTGTTTCTG 59.841 41.667 16.87 16.87 42.10 3.02
1757 1898 7.779326 TCAATATTTACTTGCAGATCCAATCCA 59.221 33.333 0.00 0.00 0.00 3.41
1758 1899 8.169977 TCAATATTTACTTGCAGATCCAATCC 57.830 34.615 0.00 0.00 0.00 3.01
1789 1930 6.620877 AATGGTAGTTGGATCTCACAGTTA 57.379 37.500 0.00 0.00 0.00 2.24
1804 1945 7.827729 GGGACTCTGTTGTTTAATAATGGTAGT 59.172 37.037 0.00 0.00 0.00 2.73
1810 1951 4.638865 GCGGGGACTCTGTTGTTTAATAAT 59.361 41.667 0.00 0.00 0.00 1.28
1880 2022 8.046504 TCAGGATGGACAGGAGTTTCCTATTG 62.047 46.154 0.00 0.00 40.59 1.90
1936 2083 1.633561 CTAGAGTGTGGCATGTGACG 58.366 55.000 0.00 0.00 0.00 4.35
1963 2110 7.012704 TGGCATATGCTCTTGAAGAATAACTTC 59.987 37.037 26.12 4.51 46.02 3.01
2091 2238 6.240549 TCTTCCTCTGAGAACCATATTTCC 57.759 41.667 6.17 0.00 0.00 3.13
2094 2241 6.183361 GGACATCTTCCTCTGAGAACCATATT 60.183 42.308 6.17 0.00 41.95 1.28
2132 2279 1.808945 CACATGGAACCAGAAGCAGAC 59.191 52.381 0.00 0.00 0.00 3.51
2175 2322 1.098050 CATTCAGCACCTTGCCCTAC 58.902 55.000 0.00 0.00 46.52 3.18
2422 2569 9.886132 GTTATTTACATAGAAGAAAGACAGGGA 57.114 33.333 0.00 0.00 0.00 4.20
2600 2747 2.691526 ACGCCGACATTGTCCTTATCTA 59.308 45.455 11.12 0.00 0.00 1.98
2623 2770 2.149578 CCTCAGGTTTTCTGCTGACTG 58.850 52.381 0.00 0.00 43.06 3.51
2642 2789 1.000938 CTCAAGCTGCAACTTGTTCCC 60.001 52.381 24.98 0.00 45.86 3.97
2673 2820 0.235926 GCAACTCAACCAGCGAAGTC 59.764 55.000 0.00 0.00 0.00 3.01
2711 2858 3.359033 TCTGGATAAAGCAAGCAAGCAT 58.641 40.909 3.19 0.00 36.85 3.79
2736 2887 4.510340 GGCTAATACGGTGAACAAGGTATG 59.490 45.833 0.00 0.00 0.00 2.39
2738 2889 3.770933 AGGCTAATACGGTGAACAAGGTA 59.229 43.478 0.00 0.00 0.00 3.08
2803 2955 5.728637 AAAAAGAATGAACATGGGAGGAC 57.271 39.130 0.00 0.00 0.00 3.85
2826 2978 8.023706 GCATCGAAGTGTACTGATATCAAGATA 58.976 37.037 6.90 0.00 0.00 1.98
2843 2995 3.255888 TCTTGTCTGTGTAGCATCGAAGT 59.744 43.478 0.00 0.00 0.00 3.01
2859 3011 8.630037 TGAAGAAGGAAAGGTTAAAATCTTGTC 58.370 33.333 0.00 0.00 27.85 3.18
2944 3096 2.672961 TAGGCTGGTTCATGACTTCG 57.327 50.000 0.00 0.00 0.00 3.79
2979 3131 2.167662 TGTAGATTCGTCCTGTGCTCA 58.832 47.619 0.00 0.00 0.00 4.26
2986 3138 4.884668 TTGTTCCTTGTAGATTCGTCCT 57.115 40.909 0.00 0.00 0.00 3.85
3072 3224 4.565652 GGTTGAAGAAAGAGGCTCCACATA 60.566 45.833 11.71 0.00 0.00 2.29
3093 3245 1.371558 GGGTTTGCGAGAGTGAGGT 59.628 57.895 0.00 0.00 0.00 3.85
3178 3330 9.005318 TCAGTTTATATCCAATGGGTAAACCTA 57.995 33.333 20.94 12.95 41.11 3.08
3263 3415 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
3264 3416 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
3265 3417 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3266 3418 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
3267 3419 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
3268 3420 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
3269 3421 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
3270 3422 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
3271 3423 6.605594 ACAAAGTTGAGTCACTTATTTTGGGA 59.394 34.615 12.94 0.00 35.87 4.37
3272 3424 6.805713 ACAAAGTTGAGTCACTTATTTTGGG 58.194 36.000 12.94 0.00 35.87 4.12
3273 3425 8.402472 TGTACAAAGTTGAGTCACTTATTTTGG 58.598 33.333 12.94 0.78 35.87 3.28
3274 3426 9.781834 TTGTACAAAGTTGAGTCACTTATTTTG 57.218 29.630 5.64 8.80 35.87 2.44
3294 3446 7.270047 ACTCAACTTTGTACTAGCTTTGTACA 58.730 34.615 21.04 21.04 45.56 2.90
3295 3447 7.437267 TGACTCAACTTTGTACTAGCTTTGTAC 59.563 37.037 17.52 17.52 40.27 2.90
3296 3448 7.437267 GTGACTCAACTTTGTACTAGCTTTGTA 59.563 37.037 0.00 0.00 0.00 2.41
3297 3449 6.258068 GTGACTCAACTTTGTACTAGCTTTGT 59.742 38.462 0.00 0.00 0.00 2.83
3298 3450 6.480320 AGTGACTCAACTTTGTACTAGCTTTG 59.520 38.462 0.00 0.00 0.00 2.77
3299 3451 6.583562 AGTGACTCAACTTTGTACTAGCTTT 58.416 36.000 0.00 0.00 0.00 3.51
3300 3452 6.163135 AGTGACTCAACTTTGTACTAGCTT 57.837 37.500 0.00 0.00 0.00 3.74
3301 3453 5.793030 AGTGACTCAACTTTGTACTAGCT 57.207 39.130 0.00 0.00 0.00 3.32
3302 3454 8.535690 AATAAGTGACTCAACTTTGTACTAGC 57.464 34.615 0.00 0.00 40.77 3.42
3308 3460 8.837389 GTCCTAAAATAAGTGACTCAACTTTGT 58.163 33.333 0.00 0.00 40.77 2.83
3309 3461 8.009974 CGTCCTAAAATAAGTGACTCAACTTTG 58.990 37.037 0.00 0.00 40.77 2.77
3310 3462 7.172703 CCGTCCTAAAATAAGTGACTCAACTTT 59.827 37.037 0.00 0.00 40.77 2.66
3311 3463 6.649557 CCGTCCTAAAATAAGTGACTCAACTT 59.350 38.462 0.00 0.00 42.89 2.66
3312 3464 6.014840 TCCGTCCTAAAATAAGTGACTCAACT 60.015 38.462 0.00 0.00 0.00 3.16
3313 3465 6.161381 TCCGTCCTAAAATAAGTGACTCAAC 58.839 40.000 0.00 0.00 0.00 3.18
3314 3466 6.349243 TCCGTCCTAAAATAAGTGACTCAA 57.651 37.500 0.00 0.00 0.00 3.02
3315 3467 5.105473 CCTCCGTCCTAAAATAAGTGACTCA 60.105 44.000 0.00 0.00 0.00 3.41
3316 3468 5.349809 CCTCCGTCCTAAAATAAGTGACTC 58.650 45.833 0.00 0.00 0.00 3.36
3317 3469 4.161754 CCCTCCGTCCTAAAATAAGTGACT 59.838 45.833 0.00 0.00 0.00 3.41
3318 3470 4.161001 TCCCTCCGTCCTAAAATAAGTGAC 59.839 45.833 0.00 0.00 0.00 3.67
3319 3471 4.355549 TCCCTCCGTCCTAAAATAAGTGA 58.644 43.478 0.00 0.00 0.00 3.41
3320 3472 4.161754 ACTCCCTCCGTCCTAAAATAAGTG 59.838 45.833 0.00 0.00 0.00 3.16
3321 3473 4.359996 ACTCCCTCCGTCCTAAAATAAGT 58.640 43.478 0.00 0.00 0.00 2.24
3322 3474 5.597594 AGTACTCCCTCCGTCCTAAAATAAG 59.402 44.000 0.00 0.00 0.00 1.73
3323 3475 5.522641 AGTACTCCCTCCGTCCTAAAATAA 58.477 41.667 0.00 0.00 0.00 1.40
3324 3476 5.134725 AGTACTCCCTCCGTCCTAAAATA 57.865 43.478 0.00 0.00 0.00 1.40
3325 3477 3.991683 AGTACTCCCTCCGTCCTAAAAT 58.008 45.455 0.00 0.00 0.00 1.82
3326 3478 3.463048 AGTACTCCCTCCGTCCTAAAA 57.537 47.619 0.00 0.00 0.00 1.52
3327 3479 3.094572 CAAGTACTCCCTCCGTCCTAAA 58.905 50.000 0.00 0.00 0.00 1.85
3328 3480 2.309755 TCAAGTACTCCCTCCGTCCTAA 59.690 50.000 0.00 0.00 0.00 2.69
3329 3481 1.918262 TCAAGTACTCCCTCCGTCCTA 59.082 52.381 0.00 0.00 0.00 2.94
3330 3482 0.702902 TCAAGTACTCCCTCCGTCCT 59.297 55.000 0.00 0.00 0.00 3.85
3331 3483 1.777941 ATCAAGTACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
3332 3484 2.496470 ACAATCAAGTACTCCCTCCGTC 59.504 50.000 0.00 0.00 0.00 4.79
3333 3485 2.233922 CACAATCAAGTACTCCCTCCGT 59.766 50.000 0.00 0.00 0.00 4.69
3334 3486 2.233922 ACACAATCAAGTACTCCCTCCG 59.766 50.000 0.00 0.00 0.00 4.63
3335 3487 3.983044 ACACAATCAAGTACTCCCTCC 57.017 47.619 0.00 0.00 0.00 4.30
3336 3488 5.153950 AGAACACAATCAAGTACTCCCTC 57.846 43.478 0.00 0.00 0.00 4.30
3337 3489 6.270231 ACTTAGAACACAATCAAGTACTCCCT 59.730 38.462 0.00 0.00 0.00 4.20
3338 3490 6.465084 ACTTAGAACACAATCAAGTACTCCC 58.535 40.000 0.00 0.00 0.00 4.30
3339 3491 6.308282 CGACTTAGAACACAATCAAGTACTCC 59.692 42.308 0.00 0.00 29.89 3.85
3340 3492 6.183359 GCGACTTAGAACACAATCAAGTACTC 60.183 42.308 0.00 0.00 29.89 2.59
3341 3493 5.634020 GCGACTTAGAACACAATCAAGTACT 59.366 40.000 0.00 0.00 29.89 2.73
3342 3494 5.634020 AGCGACTTAGAACACAATCAAGTAC 59.366 40.000 0.00 0.00 29.89 2.73
3343 3495 5.779922 AGCGACTTAGAACACAATCAAGTA 58.220 37.500 0.00 0.00 29.89 2.24
3344 3496 4.632153 AGCGACTTAGAACACAATCAAGT 58.368 39.130 0.00 0.00 32.33 3.16
3345 3497 5.377358 CAAGCGACTTAGAACACAATCAAG 58.623 41.667 0.00 0.00 0.00 3.02
3346 3498 4.319477 GCAAGCGACTTAGAACACAATCAA 60.319 41.667 0.00 0.00 0.00 2.57
3378 3531 2.038426 CCCATGAAGGACTACACACACA 59.962 50.000 0.00 0.00 41.22 3.72
3401 3562 8.555361 CCTGAAGCTTTTCTATTCTATACAAGC 58.445 37.037 0.00 0.00 36.27 4.01
3454 3615 8.547967 TTAGCTGTTTTACTCATTTCACTAGG 57.452 34.615 0.00 0.00 0.00 3.02
3473 3634 8.044060 TCTTGAATATTGTGGTTCTTTAGCTG 57.956 34.615 0.00 0.00 0.00 4.24
3619 3780 6.040166 ACAGCAGTTTGAGAAATGTCTTTCAT 59.960 34.615 0.00 0.00 42.71 2.57


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.